Starting phenix.real_space_refine on Thu Feb 5 04:46:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.map" model { file = "/net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hev_52098/02_2026/9hev_52098.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 9940 2.51 5 N 2261 2.21 5 O 2527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14819 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2117 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 4 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.59, per 1000 atoms: 0.11 Number of scatterers: 14819 At special positions: 0 Unit cell: (107.008, 109.12, 113.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2527 8.00 N 2261 7.00 C 9940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.02 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.02 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.02 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.02 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.02 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.02 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.02 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.02 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.02 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.02 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.02 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 624.0 milliseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 82.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 88 removed outlier: 3.626A pdb=" N ALA A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 90 No H-bonds generated for 'chain 'A' and resid 89 through 90' Processing helix chain 'A' and resid 100 through 100 No H-bonds generated for 'chain 'A' and resid 100 through 100' Processing helix chain 'A' and resid 101 through 131 removed outlier: 3.946A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 removed outlier: 3.688A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.630A pdb=" N LEU A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.602A pdb=" N LEU A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.769A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.626A pdb=" N ALA B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 90 No H-bonds generated for 'chain 'B' and resid 89 through 90' Processing helix chain 'B' and resid 100 through 100 No H-bonds generated for 'chain 'B' and resid 100 through 100' Processing helix chain 'B' and resid 101 through 131 removed outlier: 3.946A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 removed outlier: 3.686A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 206 through 238 removed outlier: 3.630A pdb=" N LEU B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.768A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.627A pdb=" N ALA C 78 " --> pdb=" O TRP C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 90 No H-bonds generated for 'chain 'C' and resid 89 through 90' Processing helix chain 'C' and resid 100 through 100 No H-bonds generated for 'chain 'C' and resid 100 through 100' Processing helix chain 'C' and resid 101 through 131 removed outlier: 3.946A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 removed outlier: 3.688A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 206 through 238 removed outlier: 3.630A pdb=" N LEU C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.769A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.627A pdb=" N ALA D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 90 No H-bonds generated for 'chain 'D' and resid 89 through 90' Processing helix chain 'D' and resid 100 through 100 No H-bonds generated for 'chain 'D' and resid 100 through 100' Processing helix chain 'D' and resid 101 through 131 removed outlier: 3.946A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 removed outlier: 3.687A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 206 through 238 removed outlier: 3.630A pdb=" N LEU D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.768A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 88 removed outlier: 3.626A pdb=" N ALA E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 90 No H-bonds generated for 'chain 'E' and resid 89 through 90' Processing helix chain 'E' and resid 100 through 100 No H-bonds generated for 'chain 'E' and resid 100 through 100' Processing helix chain 'E' and resid 101 through 131 removed outlier: 3.947A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 removed outlier: 3.686A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 206 through 238 removed outlier: 3.629A pdb=" N LEU E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.768A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 338 Processing helix chain 'E' and resid 341 through 354 Processing helix chain 'E' and resid 364 through 369 Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 88 removed outlier: 3.627A pdb=" N ALA F 78 " --> pdb=" O TRP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 90 No H-bonds generated for 'chain 'F' and resid 89 through 90' Processing helix chain 'F' and resid 100 through 100 No H-bonds generated for 'chain 'F' and resid 100 through 100' Processing helix chain 'F' and resid 101 through 131 removed outlier: 3.947A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 removed outlier: 3.687A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 206 through 238 removed outlier: 3.630A pdb=" N LEU F 236 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.768A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 364 through 369 Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 88 removed outlier: 3.627A pdb=" N ALA G 78 " --> pdb=" O TRP G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 90 No H-bonds generated for 'chain 'G' and resid 89 through 90' Processing helix chain 'G' and resid 100 through 100 No H-bonds generated for 'chain 'G' and resid 100 through 100' Processing helix chain 'G' and resid 101 through 131 removed outlier: 3.947A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 removed outlier: 3.687A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 206 through 238 removed outlier: 3.631A pdb=" N LEU G 236 " --> pdb=" O TYR G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 254 Processing helix chain 'G' and resid 268 through 295 removed outlier: 3.601A pdb=" N LEU G 285 " --> pdb=" O ILE G 281 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.768A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 364 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 66 1092 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4291 1.34 - 1.46: 3631 1.46 - 1.58: 7121 1.58 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 15162 Sorted by residual: bond pdb=" CB PHE E 333 " pdb=" CG PHE E 333 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.28e+00 bond pdb=" CB PHE A 333 " pdb=" CG PHE A 333 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.25e+00 bond pdb=" CB PHE F 333 " pdb=" CG PHE F 333 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.24e+00 bond pdb=" CB PHE G 333 " pdb=" CG PHE G 333 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.24e+00 bond pdb=" CB TRP A 104 " pdb=" CG TRP A 104 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.21e+00 ... (remaining 15157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 19933 2.51 - 5.03: 468 5.03 - 7.54: 123 7.54 - 10.05: 21 10.05 - 12.56: 7 Bond angle restraints: 20552 Sorted by residual: angle pdb=" CA TRP G 74 " pdb=" CB TRP G 74 " pdb=" CG TRP G 74 " ideal model delta sigma weight residual 113.60 123.06 -9.46 1.90e+00 2.77e-01 2.48e+01 angle pdb=" CA TRP F 74 " pdb=" CB TRP F 74 " pdb=" CG TRP F 74 " ideal model delta sigma weight residual 113.60 123.04 -9.44 1.90e+00 2.77e-01 2.47e+01 angle pdb=" CA TRP E 74 " pdb=" CB TRP E 74 " pdb=" CG TRP E 74 " ideal model delta sigma weight residual 113.60 123.04 -9.44 1.90e+00 2.77e-01 2.47e+01 angle pdb=" CA TRP B 74 " pdb=" CB TRP B 74 " pdb=" CG TRP B 74 " ideal model delta sigma weight residual 113.60 123.03 -9.43 1.90e+00 2.77e-01 2.46e+01 angle pdb=" CA TRP D 74 " pdb=" CB TRP D 74 " pdb=" CG TRP D 74 " ideal model delta sigma weight residual 113.60 123.02 -9.42 1.90e+00 2.77e-01 2.46e+01 ... (remaining 20547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.74: 7904 13.74 - 27.48: 846 27.48 - 41.22: 196 41.22 - 54.96: 98 54.96 - 68.71: 28 Dihedral angle restraints: 9072 sinusoidal: 3584 harmonic: 5488 Sorted by residual: dihedral pdb=" CA LEU G 252 " pdb=" C LEU G 252 " pdb=" N LYS G 253 " pdb=" CA LYS G 253 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU C 252 " pdb=" C LEU C 252 " pdb=" N LYS C 253 " pdb=" CA LYS C 253 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA LEU D 252 " pdb=" C LEU D 252 " pdb=" N LYS D 253 " pdb=" CA LYS D 253 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 9069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.062: 667 0.062 - 0.093: 351 0.093 - 0.124: 130 0.124 - 0.155: 55 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA ASN F 337 " pdb=" N ASN F 337 " pdb=" C ASN F 337 " pdb=" CB ASN F 337 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ASN C 337 " pdb=" N ASN C 337 " pdb=" C ASN C 337 " pdb=" CB ASN C 337 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ASN E 337 " pdb=" N ASN E 337 " pdb=" C ASN E 337 " pdb=" CB ASN E 337 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2461 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 104 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP F 104 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP F 104 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP F 104 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 104 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 104 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 104 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 104 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 104 " 0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP G 104 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP G 104 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP G 104 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 104 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 104 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 104 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 104 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.023 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP C 104 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.001 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 828 2.71 - 3.26: 18310 3.26 - 3.81: 27189 3.81 - 4.35: 33953 4.35 - 4.90: 51768 Nonbonded interactions: 132048 Sorted by model distance: nonbonded pdb=" O TRP E 85 " pdb=" NZ LYS E 107 " model vdw 2.163 3.120 nonbonded pdb=" O TRP A 85 " pdb=" NZ LYS A 107 " model vdw 2.163 3.120 nonbonded pdb=" O TRP F 85 " pdb=" NZ LYS F 107 " model vdw 2.164 3.120 nonbonded pdb=" O TRP G 85 " pdb=" NZ LYS G 107 " model vdw 2.164 3.120 nonbonded pdb=" O TRP D 85 " pdb=" NZ LYS D 107 " model vdw 2.164 3.120 ... (remaining 132043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15176 Z= 0.329 Angle : 1.065 12.563 20580 Z= 0.579 Chirality : 0.051 0.155 2464 Planarity : 0.007 0.079 2429 Dihedral : 13.892 68.706 5432 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.38 % Favored : 95.22 % Rotamer: Outliers : 3.73 % Allowed : 4.56 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 1757 helix: -0.85 (0.12), residues: 1246 sheet: 0.55 (0.55), residues: 77 loop : -0.82 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.004 ARG G 75 TYR 0.035 0.006 TYR D 111 PHE 0.032 0.004 PHE F 129 TRP 0.056 0.004 TRP F 104 HIS 0.006 0.002 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00642 (15162) covalent geometry : angle 1.06105 (20552) SS BOND : bond 0.00944 ( 14) SS BOND : angle 2.65286 ( 28) hydrogen bonds : bond 0.29470 ( 1092) hydrogen bonds : angle 7.46679 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 584 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.7947 (t-100) REVERT: A 144 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8202 (tp30) REVERT: A 201 THR cc_start: 0.9261 (m) cc_final: 0.8934 (m) REVERT: A 203 LYS cc_start: 0.9215 (tttt) cc_final: 0.8998 (tptt) REVERT: A 212 TYR cc_start: 0.9211 (t80) cc_final: 0.8616 (t80) REVERT: A 258 ILE cc_start: 0.9463 (mt) cc_final: 0.9071 (mt) REVERT: B 74 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7891 (t-100) REVERT: B 144 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8174 (tp30) REVERT: B 201 THR cc_start: 0.9273 (m) cc_final: 0.8874 (m) REVERT: B 203 LYS cc_start: 0.9238 (tttt) cc_final: 0.9014 (tptt) REVERT: B 212 TYR cc_start: 0.9214 (t80) cc_final: 0.8590 (t80) REVERT: B 279 ASN cc_start: 0.9511 (t0) cc_final: 0.9029 (t0) REVERT: B 352 ASN cc_start: 0.9539 (t0) cc_final: 0.9017 (t0) REVERT: C 74 TRP cc_start: 0.8362 (OUTLIER) cc_final: 0.7847 (t-100) REVERT: C 144 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8179 (tp30) REVERT: C 201 THR cc_start: 0.9238 (m) cc_final: 0.8838 (m) REVERT: C 203 LYS cc_start: 0.9239 (tttt) cc_final: 0.9009 (tptt) REVERT: C 212 TYR cc_start: 0.9197 (t80) cc_final: 0.8597 (t80) REVERT: C 352 ASN cc_start: 0.9547 (t0) cc_final: 0.9040 (t0) REVERT: D 74 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.7878 (t-100) REVERT: D 144 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8213 (tp30) REVERT: D 201 THR cc_start: 0.9279 (m) cc_final: 0.8837 (m) REVERT: D 203 LYS cc_start: 0.9243 (tttt) cc_final: 0.9006 (tptt) REVERT: D 212 TYR cc_start: 0.9244 (t80) cc_final: 0.8630 (t80) REVERT: D 352 ASN cc_start: 0.9541 (t0) cc_final: 0.9090 (t0) REVERT: E 74 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.7829 (t-100) REVERT: E 144 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8195 (tp30) REVERT: E 201 THR cc_start: 0.9277 (m) cc_final: 0.8884 (m) REVERT: E 203 LYS cc_start: 0.9256 (tttt) cc_final: 0.9020 (tptt) REVERT: E 212 TYR cc_start: 0.9230 (t80) cc_final: 0.8612 (t80) REVERT: E 352 ASN cc_start: 0.9511 (t0) cc_final: 0.9015 (t0) REVERT: F 74 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.7770 (t-100) REVERT: F 115 LEU cc_start: 0.9618 (tp) cc_final: 0.9414 (tp) REVERT: F 144 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8183 (tp30) REVERT: F 201 THR cc_start: 0.9244 (m) cc_final: 0.8889 (m) REVERT: F 203 LYS cc_start: 0.9239 (tttt) cc_final: 0.9015 (tptt) REVERT: F 212 TYR cc_start: 0.9205 (t80) cc_final: 0.8585 (t80) REVERT: F 279 ASN cc_start: 0.9496 (t0) cc_final: 0.8817 (t0) REVERT: F 283 TYR cc_start: 0.9596 (m-10) cc_final: 0.9389 (m-10) REVERT: F 352 ASN cc_start: 0.9532 (t0) cc_final: 0.9111 (t0) REVERT: G 74 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7873 (t-100) REVERT: G 144 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8136 (tp30) REVERT: G 203 LYS cc_start: 0.9265 (tttt) cc_final: 0.9048 (tptt) REVERT: G 212 TYR cc_start: 0.9213 (t80) cc_final: 0.8587 (t80) REVERT: G 279 ASN cc_start: 0.9469 (t0) cc_final: 0.8963 (t0) REVERT: G 352 ASN cc_start: 0.9517 (t0) cc_final: 0.9045 (t0) outliers start: 63 outliers final: 14 residues processed: 628 average time/residue: 0.1047 time to fit residues: 98.0459 Evaluate side-chains 471 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 450 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 247 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 279 ASN A 337 ASN B 134 HIS B 279 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 279 ASN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS E 279 ASN F 134 HIS ** F 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 279 ASN ** G 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069090 restraints weight = 76555.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.070992 restraints weight = 55667.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.072472 restraints weight = 43128.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.073606 restraints weight = 34980.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.074513 restraints weight = 29451.689| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15176 Z= 0.237 Angle : 0.940 12.408 20580 Z= 0.462 Chirality : 0.047 0.193 2464 Planarity : 0.005 0.033 2429 Dihedral : 7.681 45.025 1974 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 28.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.73 % Allowed : 22.64 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 1757 helix: -0.38 (0.11), residues: 1456 sheet: -0.31 (0.50), residues: 77 loop : 1.21 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 75 TYR 0.013 0.002 TYR A 292 PHE 0.023 0.003 PHE G 79 TRP 0.021 0.004 TRP A 104 HIS 0.008 0.003 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00465 (15162) covalent geometry : angle 0.93913 (20552) SS BOND : bond 0.00375 ( 14) SS BOND : angle 1.48565 ( 28) hydrogen bonds : bond 0.06873 ( 1092) hydrogen bonds : angle 5.66962 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 482 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9312 (t80) cc_final: 0.9104 (t80) REVERT: A 144 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8273 (tp30) REVERT: A 212 TYR cc_start: 0.9101 (t80) cc_final: 0.8621 (t80) REVERT: A 272 PHE cc_start: 0.9194 (m-10) cc_final: 0.8881 (m-10) REVERT: A 363 MET cc_start: 0.8172 (mmt) cc_final: 0.7972 (mmm) REVERT: B 37 MET cc_start: 0.8492 (mtp) cc_final: 0.8252 (mmp) REVERT: B 212 TYR cc_start: 0.9096 (t80) cc_final: 0.8736 (t80) REVERT: B 272 PHE cc_start: 0.9233 (m-10) cc_final: 0.8944 (m-10) REVERT: B 363 MET cc_start: 0.8138 (mmt) cc_final: 0.7861 (mmm) REVERT: C 37 MET cc_start: 0.8492 (mtp) cc_final: 0.8286 (mmp) REVERT: C 144 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8212 (tp30) REVERT: C 210 MET cc_start: 0.5548 (mmm) cc_final: 0.5304 (mmm) REVERT: C 212 TYR cc_start: 0.9127 (t80) cc_final: 0.8628 (t80) REVERT: C 272 PHE cc_start: 0.9203 (m-10) cc_final: 0.8926 (m-10) REVERT: C 363 MET cc_start: 0.8141 (mmt) cc_final: 0.7883 (tpp) REVERT: D 198 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.4144 (t80) REVERT: D 212 TYR cc_start: 0.9031 (t80) cc_final: 0.8497 (t80) REVERT: D 272 PHE cc_start: 0.9192 (m-10) cc_final: 0.8902 (m-10) REVERT: E 37 MET cc_start: 0.8401 (mtp) cc_final: 0.8152 (mmp) REVERT: E 121 TYR cc_start: 0.9260 (t80) cc_final: 0.9058 (t80) REVERT: E 144 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8213 (tp30) REVERT: E 198 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.4241 (t80) REVERT: E 212 TYR cc_start: 0.9106 (t80) cc_final: 0.8593 (t80) REVERT: E 247 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8411 (pt) REVERT: E 272 PHE cc_start: 0.9220 (m-10) cc_final: 0.8937 (m-10) REVERT: E 363 MET cc_start: 0.8350 (mmm) cc_final: 0.8072 (mmm) REVERT: F 37 MET cc_start: 0.8531 (mtp) cc_final: 0.8244 (mmp) REVERT: F 144 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8282 (tp30) REVERT: F 212 TYR cc_start: 0.9119 (t80) cc_final: 0.8615 (t80) REVERT: F 272 PHE cc_start: 0.9219 (m-10) cc_final: 0.8945 (m-10) REVERT: F 363 MET cc_start: 0.8137 (mmt) cc_final: 0.7846 (mmm) REVERT: G 37 MET cc_start: 0.8458 (mtp) cc_final: 0.8242 (mmp) REVERT: G 198 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.5442 (t80) REVERT: G 212 TYR cc_start: 0.9030 (t80) cc_final: 0.8500 (t80) REVERT: G 272 PHE cc_start: 0.9187 (m-10) cc_final: 0.8885 (m-10) REVERT: G 363 MET cc_start: 0.8523 (mmp) cc_final: 0.8304 (mmt) outliers start: 63 outliers final: 43 residues processed: 508 average time/residue: 0.1039 time to fit residues: 79.6078 Evaluate side-chains 445 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 141 PHE Chi-restraints excluded: chain G residue 198 TYR Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 336 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069245 restraints weight = 76934.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.071293 restraints weight = 54971.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.072817 restraints weight = 41813.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074012 restraints weight = 33532.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074969 restraints weight = 27849.569| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15176 Z= 0.209 Angle : 0.864 10.093 20580 Z= 0.422 Chirality : 0.045 0.205 2464 Planarity : 0.004 0.034 2429 Dihedral : 6.521 50.032 1948 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.62 % Allowed : 25.67 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 1757 helix: -0.04 (0.12), residues: 1456 sheet: -2.13 (0.68), residues: 42 loop : 0.29 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 75 TYR 0.016 0.002 TYR B 292 PHE 0.040 0.003 PHE C 116 TRP 0.021 0.003 TRP G 74 HIS 0.005 0.002 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00415 (15162) covalent geometry : angle 0.86334 (20552) SS BOND : bond 0.00352 ( 14) SS BOND : angle 1.15632 ( 28) hydrogen bonds : bond 0.05632 ( 1092) hydrogen bonds : angle 5.55588 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9201 (mmp) cc_final: 0.8611 (mtp) REVERT: A 116 PHE cc_start: 0.9503 (m-80) cc_final: 0.9148 (m-80) REVERT: A 121 TYR cc_start: 0.9332 (t80) cc_final: 0.9093 (t80) REVERT: A 212 TYR cc_start: 0.9132 (t80) cc_final: 0.8823 (t80) REVERT: A 241 ASP cc_start: 0.8704 (p0) cc_final: 0.7990 (m-30) REVERT: A 269 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 272 PHE cc_start: 0.9176 (m-10) cc_final: 0.8902 (m-10) REVERT: A 366 LEU cc_start: 0.8806 (mp) cc_final: 0.8504 (mp) REVERT: B 116 PHE cc_start: 0.9515 (m-80) cc_final: 0.9133 (m-80) REVERT: B 212 TYR cc_start: 0.9160 (t80) cc_final: 0.8741 (t80) REVERT: B 241 ASP cc_start: 0.8675 (p0) cc_final: 0.7911 (m-30) REVERT: B 269 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 272 PHE cc_start: 0.9221 (m-10) cc_final: 0.8962 (m-10) REVERT: B 363 MET cc_start: 0.8189 (mmt) cc_final: 0.7940 (mmm) REVERT: C 116 PHE cc_start: 0.9544 (m-80) cc_final: 0.9203 (m-80) REVERT: C 144 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8137 (tp30) REVERT: C 210 MET cc_start: 0.5609 (mmm) cc_final: 0.5352 (mmm) REVERT: C 212 TYR cc_start: 0.9157 (t80) cc_final: 0.8836 (t80) REVERT: C 241 ASP cc_start: 0.8715 (p0) cc_final: 0.7963 (m-30) REVERT: C 269 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (p) REVERT: C 272 PHE cc_start: 0.9184 (m-10) cc_final: 0.8920 (m-10) REVERT: C 363 MET cc_start: 0.8109 (mmt) cc_final: 0.7849 (tpp) REVERT: D 37 MET cc_start: 0.9274 (mmp) cc_final: 0.8700 (mtp) REVERT: D 116 PHE cc_start: 0.9542 (m-80) cc_final: 0.9195 (m-80) REVERT: D 210 MET cc_start: 0.5602 (mmm) cc_final: 0.5400 (mmm) REVERT: D 212 TYR cc_start: 0.9060 (t80) cc_final: 0.8716 (t80) REVERT: D 241 ASP cc_start: 0.8771 (p0) cc_final: 0.8000 (m-30) REVERT: D 269 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8882 (p) REVERT: D 272 PHE cc_start: 0.9190 (m-10) cc_final: 0.8902 (m-10) REVERT: E 116 PHE cc_start: 0.9562 (m-80) cc_final: 0.9215 (m-80) REVERT: E 212 TYR cc_start: 0.9122 (t80) cc_final: 0.8791 (t80) REVERT: E 241 ASP cc_start: 0.8635 (p0) cc_final: 0.7897 (m-30) REVERT: E 269 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8898 (p) REVERT: E 272 PHE cc_start: 0.9237 (m-10) cc_final: 0.8956 (m-10) REVERT: E 363 MET cc_start: 0.8305 (mmm) cc_final: 0.8017 (mmm) REVERT: F 116 PHE cc_start: 0.9533 (m-80) cc_final: 0.9205 (m-80) REVERT: F 212 TYR cc_start: 0.9172 (t80) cc_final: 0.8853 (t80) REVERT: F 241 ASP cc_start: 0.8646 (p0) cc_final: 0.7881 (m-30) REVERT: F 269 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8845 (p) REVERT: F 272 PHE cc_start: 0.9202 (m-10) cc_final: 0.8944 (m-10) REVERT: F 279 ASN cc_start: 0.9611 (t0) cc_final: 0.8961 (t0) REVERT: F 363 MET cc_start: 0.8123 (mmt) cc_final: 0.7899 (mmm) REVERT: G 116 PHE cc_start: 0.9502 (m-80) cc_final: 0.9164 (m-80) REVERT: G 210 MET cc_start: 0.5608 (mmm) cc_final: 0.5253 (mmm) REVERT: G 212 TYR cc_start: 0.9046 (t80) cc_final: 0.8550 (t80) REVERT: G 241 ASP cc_start: 0.8680 (p0) cc_final: 0.7980 (m-30) REVERT: G 269 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8823 (p) REVERT: G 272 PHE cc_start: 0.9216 (m-10) cc_final: 0.8938 (m-10) outliers start: 61 outliers final: 42 residues processed: 452 average time/residue: 0.0984 time to fit residues: 67.8643 Evaluate side-chains 444 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 395 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 111 TYR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.146333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.130149 restraints weight = 92697.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.132117 restraints weight = 47765.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.133340 restraints weight = 28499.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.134152 restraints weight = 18895.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.134662 restraints weight = 13582.206| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15176 Z= 0.203 Angle : 0.881 12.327 20580 Z= 0.427 Chirality : 0.046 0.307 2464 Planarity : 0.005 0.045 2429 Dihedral : 6.496 53.204 1946 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.10 % Allowed : 26.62 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 1757 helix: -0.08 (0.12), residues: 1456 sheet: -1.99 (0.69), residues: 42 loop : 0.79 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 128 TYR 0.020 0.002 TYR A 283 PHE 0.043 0.003 PHE D 294 TRP 0.033 0.004 TRP D 85 HIS 0.004 0.002 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00414 (15162) covalent geometry : angle 0.88055 (20552) SS BOND : bond 0.00337 ( 14) SS BOND : angle 0.96542 ( 28) hydrogen bonds : bond 0.05108 ( 1092) hydrogen bonds : angle 5.56546 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 386 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9163 (mmp) cc_final: 0.8513 (mtp) REVERT: A 116 PHE cc_start: 0.9566 (m-80) cc_final: 0.9182 (m-80) REVERT: A 210 MET cc_start: 0.5853 (mmm) cc_final: 0.5651 (mmm) REVERT: A 212 TYR cc_start: 0.8974 (t80) cc_final: 0.8624 (t80) REVERT: A 241 ASP cc_start: 0.8598 (p0) cc_final: 0.7958 (m-30) REVERT: A 269 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8805 (p) REVERT: A 272 PHE cc_start: 0.9139 (m-10) cc_final: 0.8880 (m-10) REVERT: A 279 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (t0) REVERT: B 37 MET cc_start: 0.9261 (mmp) cc_final: 0.8629 (mtp) REVERT: B 116 PHE cc_start: 0.9615 (m-80) cc_final: 0.9225 (m-80) REVERT: B 212 TYR cc_start: 0.8986 (t80) cc_final: 0.8603 (t80) REVERT: B 241 ASP cc_start: 0.8603 (p0) cc_final: 0.8010 (m-30) REVERT: B 272 PHE cc_start: 0.9141 (m-10) cc_final: 0.8887 (m-10) REVERT: B 363 MET cc_start: 0.8100 (mmt) cc_final: 0.7855 (mmm) REVERT: C 37 MET cc_start: 0.9228 (mmp) cc_final: 0.8579 (mtp) REVERT: C 116 PHE cc_start: 0.9602 (m-80) cc_final: 0.9294 (m-80) REVERT: C 144 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8175 (tp30) REVERT: C 146 LEU cc_start: 0.9055 (tp) cc_final: 0.8702 (pp) REVERT: C 210 MET cc_start: 0.5733 (mmm) cc_final: 0.5387 (mmm) REVERT: C 212 TYR cc_start: 0.8963 (t80) cc_final: 0.8603 (t80) REVERT: C 241 ASP cc_start: 0.8522 (p0) cc_final: 0.7894 (m-30) REVERT: C 269 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8790 (p) REVERT: C 272 PHE cc_start: 0.9119 (m-10) cc_final: 0.8876 (m-10) REVERT: C 363 MET cc_start: 0.8025 (mmt) cc_final: 0.7746 (mmm) REVERT: D 37 MET cc_start: 0.9251 (mmp) cc_final: 0.8606 (mtp) REVERT: D 116 PHE cc_start: 0.9603 (m-80) cc_final: 0.9296 (m-80) REVERT: D 210 MET cc_start: 0.5622 (mmm) cc_final: 0.5291 (mmm) REVERT: D 212 TYR cc_start: 0.8926 (t80) cc_final: 0.8525 (t80) REVERT: D 241 ASP cc_start: 0.8667 (p0) cc_final: 0.8064 (m-30) REVERT: D 272 PHE cc_start: 0.9119 (m-10) cc_final: 0.8855 (m-10) REVERT: E 37 MET cc_start: 0.9169 (mmp) cc_final: 0.8590 (mtp) REVERT: E 75 ARG cc_start: 0.9222 (mmp-170) cc_final: 0.8988 (mmp80) REVERT: E 112 ILE cc_start: 0.9688 (mt) cc_final: 0.9463 (tp) REVERT: E 116 PHE cc_start: 0.9625 (m-80) cc_final: 0.9186 (m-80) REVERT: E 144 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8043 (tp30) REVERT: E 210 MET cc_start: 0.5806 (mmm) cc_final: 0.5593 (mmm) REVERT: E 241 ASP cc_start: 0.8542 (p0) cc_final: 0.7883 (m-30) REVERT: E 269 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8885 (p) REVERT: E 272 PHE cc_start: 0.9144 (m-10) cc_final: 0.8898 (m-10) REVERT: E 363 MET cc_start: 0.8218 (mmm) cc_final: 0.7974 (mmm) REVERT: F 112 ILE cc_start: 0.9668 (mt) cc_final: 0.9452 (tp) REVERT: F 116 PHE cc_start: 0.9578 (m-80) cc_final: 0.9133 (m-80) REVERT: F 144 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8107 (tp30) REVERT: F 210 MET cc_start: 0.5775 (mmm) cc_final: 0.5565 (mmm) REVERT: F 212 TYR cc_start: 0.8995 (t80) cc_final: 0.8633 (t80) REVERT: F 241 ASP cc_start: 0.8550 (p0) cc_final: 0.7877 (m-30) REVERT: F 269 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8780 (p) REVERT: F 272 PHE cc_start: 0.9140 (m-10) cc_final: 0.8892 (m-10) REVERT: F 363 MET cc_start: 0.8006 (mmt) cc_final: 0.7758 (mmm) REVERT: G 37 MET cc_start: 0.9236 (mmp) cc_final: 0.8686 (mtp) REVERT: G 116 PHE cc_start: 0.9579 (m-80) cc_final: 0.9374 (m-80) REVERT: G 144 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8078 (tp30) REVERT: G 210 MET cc_start: 0.5652 (mmm) cc_final: 0.5346 (mmm) REVERT: G 212 TYR cc_start: 0.8841 (t80) cc_final: 0.8494 (t80) REVERT: G 241 ASP cc_start: 0.8565 (p0) cc_final: 0.7922 (m-30) REVERT: G 269 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8774 (p) REVERT: G 272 PHE cc_start: 0.9147 (m-10) cc_final: 0.8892 (m-10) outliers start: 86 outliers final: 50 residues processed: 441 average time/residue: 0.0959 time to fit residues: 64.7419 Evaluate side-chains 430 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 374 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 256 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 168 optimal weight: 0.0670 chunk 26 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.132524 restraints weight = 92165.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.134514 restraints weight = 47620.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.135763 restraints weight = 28457.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.136567 restraints weight = 18816.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.137084 restraints weight = 13549.834| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15176 Z= 0.187 Angle : 0.884 11.852 20580 Z= 0.422 Chirality : 0.047 0.379 2464 Planarity : 0.004 0.037 2429 Dihedral : 5.553 24.911 1932 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.68 % Allowed : 27.50 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 1757 helix: 0.26 (0.13), residues: 1449 sheet: None (None), residues: 0 loop : 0.50 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 128 TYR 0.015 0.002 TYR D 283 PHE 0.043 0.003 PHE F 294 TRP 0.048 0.004 TRP E 85 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00402 (15162) covalent geometry : angle 0.88324 (20552) SS BOND : bond 0.00460 ( 14) SS BOND : angle 1.33801 ( 28) hydrogen bonds : bond 0.04747 ( 1092) hydrogen bonds : angle 5.50914 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 410 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9112 (mmp) cc_final: 0.8479 (mtp) REVERT: A 116 PHE cc_start: 0.9487 (m-80) cc_final: 0.9165 (m-80) REVERT: A 144 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8090 (tp30) REVERT: A 210 MET cc_start: 0.5669 (mmm) cc_final: 0.5387 (mmm) REVERT: A 212 TYR cc_start: 0.8859 (t80) cc_final: 0.8492 (t80) REVERT: A 220 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9024 (p90) REVERT: A 241 ASP cc_start: 0.8369 (p0) cc_final: 0.7921 (m-30) REVERT: A 272 PHE cc_start: 0.9113 (m-10) cc_final: 0.8838 (m-10) REVERT: B 37 MET cc_start: 0.9222 (mmp) cc_final: 0.8645 (mtp) REVERT: B 116 PHE cc_start: 0.9521 (m-80) cc_final: 0.9172 (m-80) REVERT: B 212 TYR cc_start: 0.8868 (t80) cc_final: 0.8504 (t80) REVERT: B 220 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9004 (p90) REVERT: B 241 ASP cc_start: 0.8380 (p0) cc_final: 0.7858 (m-30) REVERT: B 269 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8874 (p) REVERT: B 272 PHE cc_start: 0.9114 (m-10) cc_final: 0.8851 (m-10) REVERT: B 363 MET cc_start: 0.8052 (mmt) cc_final: 0.7793 (mmm) REVERT: C 37 MET cc_start: 0.9183 (mmp) cc_final: 0.8484 (mtp) REVERT: C 116 PHE cc_start: 0.9539 (m-80) cc_final: 0.9159 (m-80) REVERT: C 144 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8180 (tp30) REVERT: C 146 LEU cc_start: 0.8970 (tp) cc_final: 0.8653 (pp) REVERT: C 210 MET cc_start: 0.5879 (mmm) cc_final: 0.5519 (mmm) REVERT: C 212 TYR cc_start: 0.8811 (t80) cc_final: 0.8446 (t80) REVERT: C 220 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.9073 (p90) REVERT: C 241 ASP cc_start: 0.8376 (p0) cc_final: 0.7858 (m-30) REVERT: C 269 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 272 PHE cc_start: 0.9096 (m-10) cc_final: 0.8829 (m-10) REVERT: C 363 MET cc_start: 0.8004 (mmt) cc_final: 0.7732 (mmm) REVERT: D 37 MET cc_start: 0.9175 (mmp) cc_final: 0.8556 (mtp) REVERT: D 116 PHE cc_start: 0.9531 (m-80) cc_final: 0.9254 (m-80) REVERT: D 144 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8096 (tp30) REVERT: D 146 LEU cc_start: 0.8967 (tp) cc_final: 0.8489 (pp) REVERT: D 210 MET cc_start: 0.5641 (mmm) cc_final: 0.5267 (mmm) REVERT: D 212 TYR cc_start: 0.8800 (t80) cc_final: 0.8403 (t80) REVERT: D 220 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9059 (p90) REVERT: D 241 ASP cc_start: 0.8479 (p0) cc_final: 0.7928 (m-30) REVERT: D 269 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8892 (p) REVERT: D 272 PHE cc_start: 0.9100 (m-10) cc_final: 0.8837 (m-10) REVERT: E 37 MET cc_start: 0.9144 (mmp) cc_final: 0.8554 (mtp) REVERT: E 116 PHE cc_start: 0.9554 (m-80) cc_final: 0.9185 (m-80) REVERT: E 210 MET cc_start: 0.5782 (mmm) cc_final: 0.5486 (mmm) REVERT: E 220 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9056 (p90) REVERT: E 241 ASP cc_start: 0.8407 (p0) cc_final: 0.7834 (m-30) REVERT: E 269 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8843 (p) REVERT: E 272 PHE cc_start: 0.9105 (m-10) cc_final: 0.8840 (m-10) REVERT: E 283 TYR cc_start: 0.9169 (m-10) cc_final: 0.8960 (m-10) REVERT: E 363 MET cc_start: 0.8103 (mmm) cc_final: 0.7817 (tpp) REVERT: F 37 MET cc_start: 0.9067 (mmp) cc_final: 0.8657 (mmm) REVERT: F 112 ILE cc_start: 0.9656 (mt) cc_final: 0.9391 (tp) REVERT: F 116 PHE cc_start: 0.9522 (m-80) cc_final: 0.9081 (m-80) REVERT: F 144 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8078 (tp30) REVERT: F 210 MET cc_start: 0.5707 (mmm) cc_final: 0.5412 (mmm) REVERT: F 212 TYR cc_start: 0.8872 (t80) cc_final: 0.8498 (t80) REVERT: F 220 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.9044 (p90) REVERT: F 241 ASP cc_start: 0.8383 (p0) cc_final: 0.7840 (m-30) REVERT: F 269 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8840 (p) REVERT: F 272 PHE cc_start: 0.9125 (m-10) cc_final: 0.8862 (m-10) REVERT: F 292 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: F 363 MET cc_start: 0.7880 (mmt) cc_final: 0.7667 (mmm) REVERT: G 37 MET cc_start: 0.9205 (mmp) cc_final: 0.8673 (mtp) REVERT: G 116 PHE cc_start: 0.9508 (m-80) cc_final: 0.9251 (m-80) REVERT: G 144 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8113 (tp30) REVERT: G 146 LEU cc_start: 0.8930 (tp) cc_final: 0.8545 (pp) REVERT: G 210 MET cc_start: 0.5800 (mmm) cc_final: 0.5460 (mmm) REVERT: G 212 TYR cc_start: 0.8732 (t80) cc_final: 0.8301 (t80) REVERT: G 220 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9048 (p90) REVERT: G 241 ASP cc_start: 0.8369 (p0) cc_final: 0.7817 (m-30) REVERT: G 269 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8843 (p) REVERT: G 272 PHE cc_start: 0.9102 (m-10) cc_final: 0.8856 (m-10) outliers start: 62 outliers final: 25 residues processed: 449 average time/residue: 0.1090 time to fit residues: 75.0128 Evaluate side-chains 413 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 292 TYR Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 197 GLN G 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.088745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071625 restraints weight = 77582.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073705 restraints weight = 55370.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.075301 restraints weight = 42047.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.076525 restraints weight = 33484.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.077502 restraints weight = 27729.749| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 15176 Z= 0.186 Angle : 0.907 11.830 20580 Z= 0.435 Chirality : 0.049 0.373 2464 Planarity : 0.004 0.036 2429 Dihedral : 5.469 24.901 1932 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.91 % Allowed : 28.87 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1757 helix: 0.48 (0.13), residues: 1414 sheet: None (None), residues: 0 loop : 0.71 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 128 TYR 0.023 0.002 TYR D 283 PHE 0.047 0.003 PHE A 294 TRP 0.038 0.004 TRP G 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00412 (15162) covalent geometry : angle 0.90645 (20552) SS BOND : bond 0.00379 ( 14) SS BOND : angle 1.30577 ( 28) hydrogen bonds : bond 0.04469 ( 1092) hydrogen bonds : angle 5.50682 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7920 (t-100) REVERT: A 144 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8107 (tp30) REVERT: A 212 TYR cc_start: 0.9172 (t80) cc_final: 0.8827 (t80) REVERT: A 220 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8941 (p90) REVERT: A 241 ASP cc_start: 0.8563 (p0) cc_final: 0.8075 (m-30) REVERT: A 272 PHE cc_start: 0.9225 (m-10) cc_final: 0.8977 (m-10) REVERT: A 279 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8886 (t0) REVERT: A 336 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: B 37 MET cc_start: 0.9264 (mmp) cc_final: 0.8680 (mtp) REVERT: B 116 PHE cc_start: 0.9480 (m-80) cc_final: 0.9119 (m-80) REVERT: B 212 TYR cc_start: 0.9161 (t80) cc_final: 0.8773 (t80) REVERT: B 220 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8924 (p90) REVERT: B 241 ASP cc_start: 0.8625 (p0) cc_final: 0.8118 (m-30) REVERT: B 272 PHE cc_start: 0.9207 (m-10) cc_final: 0.8943 (m-10) REVERT: B 332 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9115 (mt) REVERT: B 348 LYS cc_start: 0.9577 (mtmm) cc_final: 0.9275 (mmmt) REVERT: B 363 MET cc_start: 0.8285 (mmt) cc_final: 0.7974 (mmm) REVERT: C 37 MET cc_start: 0.9170 (mmp) cc_final: 0.8575 (mtp) REVERT: C 116 PHE cc_start: 0.9467 (m-80) cc_final: 0.9131 (m-80) REVERT: C 144 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8082 (tp30) REVERT: C 212 TYR cc_start: 0.9131 (t80) cc_final: 0.8788 (t80) REVERT: C 220 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8988 (p90) REVERT: C 241 ASP cc_start: 0.8584 (p0) cc_final: 0.7877 (m-30) REVERT: C 265 LYS cc_start: 0.9124 (tttt) cc_final: 0.8891 (tppt) REVERT: C 269 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8919 (p) REVERT: C 272 PHE cc_start: 0.9207 (m-10) cc_final: 0.8950 (m-10) REVERT: C 363 MET cc_start: 0.8180 (mmt) cc_final: 0.7845 (tpp) REVERT: D 37 MET cc_start: 0.9221 (mmp) cc_final: 0.8603 (mtp) REVERT: D 116 PHE cc_start: 0.9490 (m-80) cc_final: 0.9266 (m-80) REVERT: D 144 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8088 (tp30) REVERT: D 210 MET cc_start: 0.5379 (mmm) cc_final: 0.5131 (mmm) REVERT: D 212 TYR cc_start: 0.9135 (t80) cc_final: 0.8764 (t80) REVERT: D 220 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8948 (p90) REVERT: D 241 ASP cc_start: 0.8713 (p0) cc_final: 0.8104 (m-30) REVERT: D 269 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9057 (p) REVERT: D 272 PHE cc_start: 0.9207 (m-10) cc_final: 0.8963 (m-10) REVERT: E 37 MET cc_start: 0.9158 (mmp) cc_final: 0.8608 (mtp) REVERT: E 116 PHE cc_start: 0.9538 (m-80) cc_final: 0.9207 (m-80) REVERT: E 144 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8029 (tp30) REVERT: E 210 MET cc_start: 0.5510 (mmm) cc_final: 0.5309 (mmm) REVERT: E 220 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8988 (p90) REVERT: E 241 ASP cc_start: 0.8666 (p0) cc_final: 0.8067 (m-30) REVERT: E 269 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.9005 (p) REVERT: E 272 PHE cc_start: 0.9214 (m-10) cc_final: 0.8966 (m-10) REVERT: E 363 MET cc_start: 0.8259 (mmm) cc_final: 0.7954 (mmm) REVERT: F 37 MET cc_start: 0.9115 (mmp) cc_final: 0.8746 (mmm) REVERT: F 144 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8041 (tp30) REVERT: F 210 MET cc_start: 0.5348 (mmm) cc_final: 0.5139 (mmm) REVERT: F 220 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8967 (p90) REVERT: F 241 ASP cc_start: 0.8684 (p0) cc_final: 0.8046 (m-30) REVERT: F 265 LYS cc_start: 0.9274 (tttt) cc_final: 0.9063 (tppt) REVERT: F 269 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9035 (p) REVERT: F 272 PHE cc_start: 0.9224 (m-10) cc_final: 0.8980 (m-10) REVERT: F 292 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.5764 (m-10) REVERT: F 363 MET cc_start: 0.8065 (mmt) cc_final: 0.7800 (mmm) REVERT: G 37 MET cc_start: 0.9256 (mmp) cc_final: 0.8752 (mtp) REVERT: G 144 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8053 (tp30) REVERT: G 210 MET cc_start: 0.5550 (mmm) cc_final: 0.5338 (mmm) REVERT: G 212 TYR cc_start: 0.9056 (t80) cc_final: 0.8654 (t80) REVERT: G 220 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8964 (p90) REVERT: G 241 ASP cc_start: 0.8683 (p0) cc_final: 0.8207 (m-30) REVERT: G 265 LYS cc_start: 0.9411 (tttt) cc_final: 0.8652 (ttmm) REVERT: G 272 PHE cc_start: 0.9166 (m-10) cc_final: 0.8913 (m-10) REVERT: G 279 ASN cc_start: 0.9494 (OUTLIER) cc_final: 0.8747 (t0) outliers start: 66 outliers final: 36 residues processed: 419 average time/residue: 0.1067 time to fit residues: 67.6406 Evaluate side-chains 411 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 358 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 292 TYR Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.087735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070422 restraints weight = 76736.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072538 restraints weight = 54396.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074171 restraints weight = 41116.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075428 restraints weight = 32642.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.076431 restraints weight = 26961.748| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15176 Z= 0.195 Angle : 0.923 12.185 20580 Z= 0.444 Chirality : 0.050 0.400 2464 Planarity : 0.004 0.034 2429 Dihedral : 5.399 24.714 1932 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.98 % Allowed : 29.34 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1757 helix: 0.53 (0.13), residues: 1379 sheet: None (None), residues: 0 loop : 1.05 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 128 TYR 0.025 0.002 TYR D 283 PHE 0.060 0.003 PHE G 116 TRP 0.049 0.005 TRP D 85 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00431 (15162) covalent geometry : angle 0.92231 (20552) SS BOND : bond 0.00450 ( 14) SS BOND : angle 1.43593 ( 28) hydrogen bonds : bond 0.04410 ( 1092) hydrogen bonds : angle 5.49880 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9112 (mmp) cc_final: 0.8440 (mtp) REVERT: A 74 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7983 (t-100) REVERT: A 144 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8059 (tp30) REVERT: A 212 TYR cc_start: 0.9144 (t80) cc_final: 0.8811 (t80) REVERT: A 220 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8953 (p90) REVERT: A 241 ASP cc_start: 0.8606 (p0) cc_final: 0.8157 (m-30) REVERT: A 272 PHE cc_start: 0.9242 (m-10) cc_final: 0.8973 (m-10) REVERT: A 292 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5776 (m-10) REVERT: A 336 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: B 37 MET cc_start: 0.9249 (mmp) cc_final: 0.8733 (mtp) REVERT: B 64 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9023 (mp) REVERT: B 212 TYR cc_start: 0.9129 (t80) cc_final: 0.8765 (t80) REVERT: B 220 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8899 (p90) REVERT: B 241 ASP cc_start: 0.8584 (p0) cc_final: 0.8131 (m-30) REVERT: B 272 PHE cc_start: 0.9233 (m-10) cc_final: 0.8987 (m-10) REVERT: B 292 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5934 (m-10) REVERT: B 363 MET cc_start: 0.8307 (mmt) cc_final: 0.7996 (mmm) REVERT: C 37 MET cc_start: 0.9160 (mmp) cc_final: 0.8488 (mtm) REVERT: C 112 ILE cc_start: 0.9583 (mm) cc_final: 0.9314 (mm) REVERT: C 116 PHE cc_start: 0.9468 (m-80) cc_final: 0.9186 (m-80) REVERT: C 144 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8089 (tp30) REVERT: C 212 TYR cc_start: 0.9115 (t80) cc_final: 0.8766 (t80) REVERT: C 220 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8959 (p90) REVERT: C 241 ASP cc_start: 0.8632 (p0) cc_final: 0.8118 (m-30) REVERT: C 269 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9015 (p) REVERT: C 272 PHE cc_start: 0.9249 (m-10) cc_final: 0.8997 (m-10) REVERT: C 292 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5605 (m-10) REVERT: C 348 LYS cc_start: 0.9578 (mtmm) cc_final: 0.9272 (mmmt) REVERT: C 363 MET cc_start: 0.8237 (mmt) cc_final: 0.7941 (mmm) REVERT: D 144 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8112 (tp30) REVERT: D 203 LYS cc_start: 0.9188 (pttt) cc_final: 0.8974 (pptt) REVERT: D 210 MET cc_start: 0.5334 (mmm) cc_final: 0.5074 (mmm) REVERT: D 220 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8942 (p90) REVERT: D 241 ASP cc_start: 0.8762 (p0) cc_final: 0.8179 (m-30) REVERT: D 269 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9054 (p) REVERT: D 272 PHE cc_start: 0.9227 (m-10) cc_final: 0.8974 (m-10) REVERT: D 279 ASN cc_start: 0.9316 (m-40) cc_final: 0.8921 (m110) REVERT: D 292 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: E 37 MET cc_start: 0.9153 (mmp) cc_final: 0.8599 (mtp) REVERT: E 116 PHE cc_start: 0.9565 (m-80) cc_final: 0.9220 (m-80) REVERT: E 210 MET cc_start: 0.5458 (mmm) cc_final: 0.5238 (mmm) REVERT: E 220 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8970 (p90) REVERT: E 241 ASP cc_start: 0.8646 (p0) cc_final: 0.8164 (m-30) REVERT: E 265 LYS cc_start: 0.9234 (tttt) cc_final: 0.8422 (ttmt) REVERT: E 272 PHE cc_start: 0.9256 (m-10) cc_final: 0.8991 (m-10) REVERT: E 292 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: E 332 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9124 (mt) REVERT: E 363 MET cc_start: 0.8266 (mmm) cc_final: 0.7988 (mmm) REVERT: F 37 MET cc_start: 0.9107 (mmp) cc_final: 0.8732 (mmm) REVERT: F 144 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8053 (tp30) REVERT: F 210 MET cc_start: 0.5297 (mmm) cc_final: 0.5087 (mmm) REVERT: F 220 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8968 (p90) REVERT: F 241 ASP cc_start: 0.8726 (p0) cc_final: 0.8258 (m-30) REVERT: F 272 PHE cc_start: 0.9256 (m-10) cc_final: 0.9006 (m-10) REVERT: F 292 TYR cc_start: 0.5983 (OUTLIER) cc_final: 0.5709 (m-10) REVERT: F 363 MET cc_start: 0.8103 (mmt) cc_final: 0.7835 (mmm) REVERT: G 37 MET cc_start: 0.9263 (mmp) cc_final: 0.8757 (mtp) REVERT: G 144 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8126 (mm-30) REVERT: G 210 MET cc_start: 0.5526 (mmm) cc_final: 0.5313 (mmm) REVERT: G 212 TYR cc_start: 0.9047 (t80) cc_final: 0.8652 (t80) REVERT: G 220 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.9002 (p90) REVERT: G 241 ASP cc_start: 0.8645 (p0) cc_final: 0.8122 (m-30) REVERT: G 269 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9017 (p) REVERT: G 272 PHE cc_start: 0.9211 (m-10) cc_final: 0.8968 (m-10) REVERT: G 279 ASN cc_start: 0.9517 (t0) cc_final: 0.9306 (m-40) REVERT: G 292 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5948 (m-80) outliers start: 84 outliers final: 46 residues processed: 426 average time/residue: 0.1055 time to fit residues: 67.3581 Evaluate side-chains 426 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 85 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 292 TYR Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 292 TYR Chi-restraints excluded: chain G residue 334 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 135 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.089042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071535 restraints weight = 75418.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073758 restraints weight = 52789.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075400 restraints weight = 39534.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076719 restraints weight = 31440.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077774 restraints weight = 25768.084| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15176 Z= 0.182 Angle : 0.959 12.864 20580 Z= 0.455 Chirality : 0.050 0.409 2464 Planarity : 0.004 0.034 2429 Dihedral : 5.378 24.243 1932 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 30.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 5.22 % Allowed : 30.47 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1757 helix: 0.54 (0.13), residues: 1372 sheet: None (None), residues: 0 loop : 1.00 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 128 TYR 0.032 0.001 TYR D 283 PHE 0.053 0.003 PHE G 116 TRP 0.048 0.004 TRP C 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00406 (15162) covalent geometry : angle 0.95785 (20552) SS BOND : bond 0.00374 ( 14) SS BOND : angle 1.70874 ( 28) hydrogen bonds : bond 0.04243 ( 1092) hydrogen bonds : angle 5.50961 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 371 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9107 (mmp) cc_final: 0.8433 (mtp) REVERT: A 212 TYR cc_start: 0.9150 (t80) cc_final: 0.8833 (t80) REVERT: A 220 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8931 (p90) REVERT: A 241 ASP cc_start: 0.8613 (p0) cc_final: 0.8162 (m-30) REVERT: A 272 PHE cc_start: 0.9240 (m-10) cc_final: 0.8980 (m-10) REVERT: A 292 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5854 (m-10) REVERT: B 37 MET cc_start: 0.9205 (mmp) cc_final: 0.8691 (mtp) REVERT: B 64 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9059 (mp) REVERT: B 116 PHE cc_start: 0.9456 (m-80) cc_final: 0.9234 (m-80) REVERT: B 128 ARG cc_start: 0.9586 (ptt-90) cc_final: 0.9322 (ptt90) REVERT: B 212 TYR cc_start: 0.9159 (t80) cc_final: 0.8783 (t80) REVERT: B 220 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8931 (p90) REVERT: B 241 ASP cc_start: 0.8547 (p0) cc_final: 0.8124 (m-30) REVERT: B 272 PHE cc_start: 0.9238 (m-10) cc_final: 0.9001 (m-10) REVERT: B 292 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5940 (m-10) REVERT: B 363 MET cc_start: 0.8318 (mmt) cc_final: 0.7977 (mmm) REVERT: C 37 MET cc_start: 0.9168 (mmp) cc_final: 0.8531 (mtm) REVERT: C 144 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8087 (tp30) REVERT: C 212 TYR cc_start: 0.9139 (t80) cc_final: 0.8798 (t80) REVERT: C 220 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8919 (p90) REVERT: C 241 ASP cc_start: 0.8744 (p0) cc_final: 0.8228 (m-30) REVERT: C 269 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9003 (p) REVERT: C 272 PHE cc_start: 0.9272 (m-10) cc_final: 0.8995 (m-10) REVERT: C 292 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.5571 (m-10) REVERT: C 363 MET cc_start: 0.8249 (mmt) cc_final: 0.7948 (mmm) REVERT: D 37 MET cc_start: 0.9142 (mmp) cc_final: 0.8527 (mtp) REVERT: D 144 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8102 (tp30) REVERT: D 203 LYS cc_start: 0.9206 (pttt) cc_final: 0.8991 (pptt) REVERT: D 210 MET cc_start: 0.5221 (mmm) cc_final: 0.4991 (mmm) REVERT: D 220 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8905 (p90) REVERT: D 265 LYS cc_start: 0.9139 (tttt) cc_final: 0.8614 (ttmt) REVERT: D 269 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9021 (p) REVERT: D 272 PHE cc_start: 0.9246 (m-10) cc_final: 0.9019 (m-10) REVERT: D 279 ASN cc_start: 0.9208 (m-40) cc_final: 0.8903 (m110) REVERT: E 37 MET cc_start: 0.9137 (mmp) cc_final: 0.8593 (mtp) REVERT: E 116 PHE cc_start: 0.9569 (m-80) cc_final: 0.9314 (m-80) REVERT: E 210 MET cc_start: 0.5269 (mmm) cc_final: 0.5062 (mmm) REVERT: E 220 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8943 (p90) REVERT: E 241 ASP cc_start: 0.8640 (p0) cc_final: 0.8101 (m-30) REVERT: E 269 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9009 (p) REVERT: E 272 PHE cc_start: 0.9265 (m-10) cc_final: 0.9019 (m-10) REVERT: E 292 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5856 (m-10) REVERT: E 332 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9093 (mt) REVERT: E 363 MET cc_start: 0.8260 (mmm) cc_final: 0.7990 (mmm) REVERT: F 37 MET cc_start: 0.9099 (mmp) cc_final: 0.8728 (mmm) REVERT: F 144 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8011 (tp30) REVERT: F 210 MET cc_start: 0.5166 (mmm) cc_final: 0.4966 (mmm) REVERT: F 220 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8951 (p90) REVERT: F 241 ASP cc_start: 0.8735 (p0) cc_final: 0.8223 (m-30) REVERT: F 269 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.8996 (p) REVERT: F 272 PHE cc_start: 0.9271 (m-10) cc_final: 0.9032 (m-10) REVERT: F 363 MET cc_start: 0.8106 (mmt) cc_final: 0.7755 (tpp) REVERT: G 37 MET cc_start: 0.9247 (mmp) cc_final: 0.8755 (mtp) REVERT: G 144 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8074 (tp30) REVERT: G 212 TYR cc_start: 0.9087 (t80) cc_final: 0.8725 (t80) REVERT: G 220 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.9036 (p90) REVERT: G 241 ASP cc_start: 0.8638 (p0) cc_final: 0.8208 (m-30) REVERT: G 265 LYS cc_start: 0.9320 (tttt) cc_final: 0.8619 (ttmt) REVERT: G 269 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.8942 (p) REVERT: G 272 PHE cc_start: 0.9235 (m-10) cc_final: 0.8985 (m-10) REVERT: G 292 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.5928 (m-80) outliers start: 88 outliers final: 57 residues processed: 427 average time/residue: 0.1090 time to fit residues: 69.8571 Evaluate side-chains 437 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 361 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 111 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 292 TYR Chi-restraints excluded: chain G residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 167 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.089103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.072284 restraints weight = 77669.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074279 restraints weight = 56429.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.075797 restraints weight = 43130.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.077002 restraints weight = 34488.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.077967 restraints weight = 28595.393| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15176 Z= 0.188 Angle : 0.984 13.011 20580 Z= 0.468 Chirality : 0.051 0.408 2464 Planarity : 0.004 0.034 2429 Dihedral : 5.371 23.590 1932 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.10 % Allowed : 31.06 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1757 helix: 0.49 (0.13), residues: 1372 sheet: None (None), residues: 0 loop : 1.25 (0.35), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 128 TYR 0.027 0.002 TYR D 283 PHE 0.061 0.004 PHE F 116 TRP 0.048 0.004 TRP C 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00420 (15162) covalent geometry : angle 0.98215 (20552) SS BOND : bond 0.00370 ( 14) SS BOND : angle 1.89602 ( 28) hydrogen bonds : bond 0.04213 ( 1092) hydrogen bonds : angle 5.53100 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 365 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9087 (mmp) cc_final: 0.8427 (mtp) REVERT: A 212 TYR cc_start: 0.9125 (t80) cc_final: 0.8782 (t80) REVERT: A 220 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8946 (p90) REVERT: A 241 ASP cc_start: 0.8536 (p0) cc_final: 0.8159 (m-30) REVERT: A 272 PHE cc_start: 0.9201 (m-10) cc_final: 0.8954 (m-10) REVERT: A 292 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5920 (m-10) REVERT: B 37 MET cc_start: 0.9168 (mmp) cc_final: 0.8626 (mtp) REVERT: B 64 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 116 PHE cc_start: 0.9418 (m-80) cc_final: 0.9140 (m-80) REVERT: B 128 ARG cc_start: 0.9563 (ptt-90) cc_final: 0.9271 (ptt90) REVERT: B 212 TYR cc_start: 0.9131 (t80) cc_final: 0.8755 (t80) REVERT: B 220 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8886 (p90) REVERT: B 241 ASP cc_start: 0.8462 (p0) cc_final: 0.8037 (m-30) REVERT: B 269 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 272 PHE cc_start: 0.9235 (m-10) cc_final: 0.8976 (m-10) REVERT: B 292 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: B 348 LYS cc_start: 0.9586 (mtmm) cc_final: 0.9251 (mmmt) REVERT: B 363 MET cc_start: 0.8364 (mmt) cc_final: 0.8018 (mmm) REVERT: C 37 MET cc_start: 0.9170 (mmp) cc_final: 0.8549 (mtm) REVERT: C 144 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8101 (tp30) REVERT: C 212 TYR cc_start: 0.9109 (t80) cc_final: 0.8774 (t80) REVERT: C 220 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8914 (p90) REVERT: C 241 ASP cc_start: 0.8682 (p0) cc_final: 0.8233 (m-30) REVERT: C 269 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9005 (p) REVERT: C 272 PHE cc_start: 0.9255 (m-10) cc_final: 0.9003 (m-10) REVERT: C 292 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5622 (m-10) REVERT: C 348 LYS cc_start: 0.9568 (mtmm) cc_final: 0.9229 (mmmt) REVERT: C 363 MET cc_start: 0.8270 (mmt) cc_final: 0.7928 (tpp) REVERT: D 37 MET cc_start: 0.9115 (mmp) cc_final: 0.8498 (mtp) REVERT: D 112 ILE cc_start: 0.9605 (mm) cc_final: 0.9399 (mt) REVERT: D 144 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8129 (tp30) REVERT: D 203 LYS cc_start: 0.9228 (pttt) cc_final: 0.9014 (pptt) REVERT: D 210 MET cc_start: 0.5306 (mmm) cc_final: 0.5090 (mmm) REVERT: D 220 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8892 (p90) REVERT: D 265 LYS cc_start: 0.9245 (tttt) cc_final: 0.8683 (ttmt) REVERT: D 269 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9029 (p) REVERT: D 272 PHE cc_start: 0.9225 (m-10) cc_final: 0.8991 (m-10) REVERT: D 292 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: E 37 MET cc_start: 0.9138 (mmp) cc_final: 0.8591 (mtp) REVERT: E 116 PHE cc_start: 0.9523 (m-80) cc_final: 0.9273 (m-80) REVERT: E 210 MET cc_start: 0.5344 (mmm) cc_final: 0.5118 (mmm) REVERT: E 220 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8943 (p90) REVERT: E 241 ASP cc_start: 0.8543 (p0) cc_final: 0.7994 (m-30) REVERT: E 265 LYS cc_start: 0.9327 (tttt) cc_final: 0.9096 (tppt) REVERT: E 269 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.8983 (p) REVERT: E 272 PHE cc_start: 0.9239 (m-10) cc_final: 0.8976 (m-10) REVERT: E 292 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5870 (m-10) REVERT: E 363 MET cc_start: 0.8287 (mmm) cc_final: 0.8011 (mmm) REVERT: F 47 LEU cc_start: 0.9642 (tp) cc_final: 0.9389 (pp) REVERT: F 144 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8021 (tp30) REVERT: F 210 MET cc_start: 0.5302 (mmm) cc_final: 0.5098 (mmm) REVERT: F 220 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8979 (p90) REVERT: F 241 ASP cc_start: 0.8659 (p0) cc_final: 0.8219 (m-30) REVERT: F 269 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.8990 (p) REVERT: F 272 PHE cc_start: 0.9243 (m-10) cc_final: 0.9001 (m-10) REVERT: F 292 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5649 (m-10) REVERT: F 332 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9032 (mt) REVERT: F 363 MET cc_start: 0.8164 (mmt) cc_final: 0.7788 (tpp) REVERT: G 37 MET cc_start: 0.9242 (mmp) cc_final: 0.8735 (mtp) REVERT: G 144 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8077 (tp30) REVERT: G 212 TYR cc_start: 0.9054 (t80) cc_final: 0.8697 (t80) REVERT: G 220 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9009 (p90) REVERT: G 241 ASP cc_start: 0.8572 (p0) cc_final: 0.8176 (m-30) REVERT: G 269 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (p) REVERT: G 272 PHE cc_start: 0.9206 (m-10) cc_final: 0.8968 (m-10) REVERT: G 279 ASN cc_start: 0.9428 (m-40) cc_final: 0.8895 (m110) REVERT: G 283 TYR cc_start: 0.9354 (m-10) cc_final: 0.9148 (m-80) REVERT: G 292 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5921 (m-80) outliers start: 86 outliers final: 56 residues processed: 423 average time/residue: 0.1093 time to fit residues: 70.0821 Evaluate side-chains 429 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 111 TYR Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 292 TYR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 292 TYR Chi-restraints excluded: chain G residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 90 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.092233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.074911 restraints weight = 75180.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.076973 restraints weight = 54180.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.078606 restraints weight = 41513.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.079825 restraints weight = 33125.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080815 restraints weight = 27527.846| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15176 Z= 0.172 Angle : 1.027 14.076 20580 Z= 0.478 Chirality : 0.052 0.417 2464 Planarity : 0.004 0.037 2429 Dihedral : 5.278 22.566 1932 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.73 % Allowed : 32.54 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1757 helix: 0.59 (0.13), residues: 1372 sheet: None (None), residues: 0 loop : 1.44 (0.37), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 128 TYR 0.036 0.001 TYR A 283 PHE 0.059 0.003 PHE F 116 TRP 0.057 0.004 TRP A 74 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00381 (15162) covalent geometry : angle 1.02595 (20552) SS BOND : bond 0.00374 ( 14) SS BOND : angle 1.60988 ( 28) hydrogen bonds : bond 0.04085 ( 1092) hydrogen bonds : angle 5.43921 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 372 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.9124 (t80) cc_final: 0.8802 (t80) REVERT: A 220 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8866 (p90) REVERT: A 241 ASP cc_start: 0.8451 (p0) cc_final: 0.8088 (m-30) REVERT: A 272 PHE cc_start: 0.9176 (m-10) cc_final: 0.8935 (m-10) REVERT: A 292 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5881 (m-10) REVERT: A 336 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: B 37 MET cc_start: 0.9149 (mmp) cc_final: 0.8572 (mtp) REVERT: B 64 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8963 (mp) REVERT: B 128 ARG cc_start: 0.9586 (ptt-90) cc_final: 0.9295 (ptt90) REVERT: B 212 TYR cc_start: 0.9112 (t80) cc_final: 0.8743 (t80) REVERT: B 220 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8824 (p90) REVERT: B 241 ASP cc_start: 0.8329 (p0) cc_final: 0.7925 (m-30) REVERT: B 269 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8965 (p) REVERT: B 272 PHE cc_start: 0.9208 (m-10) cc_final: 0.8958 (m-10) REVERT: B 292 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: B 348 LYS cc_start: 0.9581 (mtmm) cc_final: 0.9257 (mmmt) REVERT: B 363 MET cc_start: 0.8325 (mmt) cc_final: 0.7951 (mmm) REVERT: C 37 MET cc_start: 0.9157 (mmp) cc_final: 0.8560 (mtm) REVERT: C 144 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8033 (tp30) REVERT: C 212 TYR cc_start: 0.9094 (t80) cc_final: 0.8754 (t80) REVERT: C 220 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8900 (p90) REVERT: C 272 PHE cc_start: 0.9221 (m-10) cc_final: 0.8957 (m-10) REVERT: C 292 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5608 (m-10) REVERT: C 348 LYS cc_start: 0.9565 (mtmm) cc_final: 0.9285 (mmmt) REVERT: C 363 MET cc_start: 0.8237 (mmt) cc_final: 0.7886 (tpp) REVERT: D 37 MET cc_start: 0.9112 (mmp) cc_final: 0.8505 (mtp) REVERT: D 144 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8069 (tp30) REVERT: D 203 LYS cc_start: 0.9197 (pttt) cc_final: 0.8994 (pptt) REVERT: D 220 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8883 (p90) REVERT: D 269 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9047 (p) REVERT: D 272 PHE cc_start: 0.9203 (m-10) cc_final: 0.8980 (m-10) REVERT: E 37 MET cc_start: 0.9128 (mmp) cc_final: 0.8573 (mtp) REVERT: E 220 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8952 (p90) REVERT: E 269 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9040 (p) REVERT: E 272 PHE cc_start: 0.9229 (m-10) cc_final: 0.8983 (m-10) REVERT: E 292 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: E 294 PHE cc_start: 0.8729 (m-80) cc_final: 0.8501 (m-80) REVERT: E 363 MET cc_start: 0.8238 (mmm) cc_final: 0.7990 (mmm) REVERT: F 47 LEU cc_start: 0.9615 (tp) cc_final: 0.9375 (pp) REVERT: F 220 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8955 (p90) REVERT: F 269 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9007 (p) REVERT: F 272 PHE cc_start: 0.9214 (m-10) cc_final: 0.8975 (m-10) REVERT: F 279 ASN cc_start: 0.9463 (m-40) cc_final: 0.9002 (m110) REVERT: F 292 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5622 (m-10) REVERT: F 332 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9031 (mt) REVERT: F 363 MET cc_start: 0.8116 (mmt) cc_final: 0.7675 (tpp) REVERT: G 37 MET cc_start: 0.9244 (mmp) cc_final: 0.8726 (mtp) REVERT: G 144 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8066 (tp30) REVERT: G 212 TYR cc_start: 0.9047 (t80) cc_final: 0.8717 (t80) REVERT: G 220 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8978 (p90) REVERT: G 265 LYS cc_start: 0.9191 (tttt) cc_final: 0.8548 (ttmt) REVERT: G 269 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9015 (p) REVERT: G 272 PHE cc_start: 0.9215 (m-10) cc_final: 0.8968 (m-10) REVERT: G 279 ASN cc_start: 0.9375 (m-40) cc_final: 0.8735 (m110) outliers start: 63 outliers final: 38 residues processed: 415 average time/residue: 0.1145 time to fit residues: 71.1917 Evaluate side-chains 414 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 356 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 220 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 292 TYR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 220 PHE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 104 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.090318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072602 restraints weight = 74955.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.074599 restraints weight = 55072.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.076142 restraints weight = 42774.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.077348 restraints weight = 34703.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.078312 restraints weight = 29133.444| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15176 Z= 0.191 Angle : 1.011 15.507 20580 Z= 0.480 Chirality : 0.052 0.410 2464 Planarity : 0.005 0.036 2429 Dihedral : 5.271 21.530 1932 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 31.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.21 % Allowed : 32.78 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1757 helix: 0.52 (0.13), residues: 1379 sheet: None (None), residues: 0 loop : 1.64 (0.37), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 128 TYR 0.025 0.002 TYR D 283 PHE 0.065 0.004 PHE C 116 TRP 0.055 0.005 TRP A 74 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00430 (15162) covalent geometry : angle 1.00966 (20552) SS BOND : bond 0.00454 ( 14) SS BOND : angle 1.72015 ( 28) hydrogen bonds : bond 0.04128 ( 1092) hydrogen bonds : angle 5.54962 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.50 seconds wall clock time: 45 minutes 10.18 seconds (2710.18 seconds total)